¿Qué es la Investigación Reproducible?

Etapas de una Investigación Reproducible

Ciencia Abierta

Espectro de Reproducibilidad

Repositorio

R project

https://cran.dcc.uchile.cl/

RSudio IDE

https://posit.co/download/rstudio-desktop/

Existen otras alternativas más génericas como Visual Studio Code, un editor de código para múltiples lenguajes. Sin embargo, al no ser un software especializado en R, requiere utilizar extensiones para lograr las funcionalidad que otorga RStudio.

Quarto

https://quarto.org/docs/get-started/

Git & Github

• Cuenta en GitHub

• Github Desktop

Rmarkdown & Quarto

Algunos ejemplos

• Galería de ejemplos

Quarto

Los archivos Quarto fueron diseñados para ser usados de tres maneras:

1. Para comunicar a los tomadores de decisiones, quienes quieren centrarse en las conclusiones, no en el código detrás del análisis.

2. Para colaborar con otros investigadores, quienes están interesados en las conclusiones y el cómo se llego a ellas (i.e. el código)

3. Como un ambiente para hacer análisis, como un notebook donde se puede capturar el trabajo realizado junto a notas de este.

Primeros pasos

1. Entrar a Quarto.org
2. Descargar Quarto para tu sistema operativo
3. Ingresar a RStudio y crear documento .qmd

Flujo documento Quarto

• qmd: archivo de origen
• knitr: Herramienta que interpreta y ejecuta códigos y lo traduce en texto markdown
• md: texto escrito en lenguaje markdown
• pandoc: Herramienta que convierte archivos .md enb distintos formatos

Anatomía de un documento Quarto

1. Encabezado en formato YAML
2. Texto en formato Quarto
3. Bloques de código (R, Python, Julia, Observable)

YAML

YAML es un formato de serialización de datos que puede ser leído fácilmente. Su uso es amplio, desde Acciones en GitHub hasta Quarto

Un ejemplo de YAML que difine un ambiente computacional podría ser:

# Define the operating system as Linux
os: linux

# Use the xenial distribution of Linux
dist: xenial

# Use the programming language Python
language: python

# Use version of Python 3.2
python: 3.2

Herramientas

El contenido del documento puede estar escrito utilizando diferentes formatos, entre ellos:

• Quarto
• HTML
• LaTeX
• CSS

Creación de documento básico

1. Abrir RStudio
2. File > New File > Quarto Document
3. Definir características del documento

Formato de Texto

*italics*, **bold**, ***bold italics***

superscript^2^ / subscript~2~

~~strikethrough~~

`verbatim code`

Encabezados

# Header 1

## Header 2

### Header 3

#### Header 4

##### Header 5

###### Header 6

Listas

(@)  Una lista cuyos números

continuan después

(@)  de una interrupción

::: {}
1. Una lista
:::

::: {}
1. Seguida de otra lista
:::

término
: definición

Tablas

Sintáxis Markdown

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

Output

Código de fuente

Usamos ``` para delimitar bloques de código:

```
código
```

Podemos agregar un lenguaje para destacar el código:

```python
1 + 1
```

Pandoc ofrece 140 distintos lenguajes para destacar código.

Guía de referencia

Para una lista exhaustiva de las opciones de formato que tienen los documentos .qmd visitar https://quarto.org/docs/guide/.

Formatos de salida: Documentos

Los formatos de salida más utilizados para documentos creados con Quarto son:

• HTML
• PDF
• DOCX

Formatos de salida: Presentaciones

En Quarto tenemos 3 opciones para presentaciones:

• RevealJS
• PowerPoint
• Beamer

En donde RevealJS es el formato que nos entrega más herramientas. (Esta presentación fue hecha utilizando RevealJS en Quarto)

Caso práctico

Awesome Quarto

Este tutorial

Este tutorial usa un template llamado clean. Está disponible en un repositorio en GitHub.

Example slide

This is a subtitle

Before we dive a bit deeper, here is a simple example of the clean theme in action.

• No pictures or anything fancy. Just text for the moment.

Next, we’ll take a brief tour of some theme components.

• We’ll use the same basic structure as the original LaTeX slides.
• Note that the full suite of Reveal.js features are available for this Quarto implementation, even if we don’t cover everything here.

Before you proceed…

Requirements for the coding examples in this demo

The clean theme is language agnostic. Use it with R, Python, Julia, etc. Or none of the above.

However, this demo uses R code to highlight advanced theme features. You’ll need to install some software if you’d like to render the demo “as-is”.

install.packages(c("modelsummary", "fixest", "pdftools", "tinytex", "threejs"))

quarto install tinytex

Components

Ordered and Unordered Lists

Here we have an unordered list.

• first item
  • sub-item
• second item

And next we have an ordered one.

1. first item
   1. sub-item
2. second item

Components

Alerts & Cross-refs

To emphasize specific words or text, you can:

• Use the default .alert class, e.g. important note.
• Use the .fg class for custom colour, e.g. important note.
• Use the .bg class for custom background, e.g. important note.

To cross-reference, you have several options, for example:

• Beamer-like .button class provided by this theme, e.g. Appendix
• Quarto’s native cross-ref syntax, e.g., “See Sección 15.3.”

Components

Citations

Citations follow the standard Quarto format and be sourced from BibLaTex, BibTeX, or CLS files. For example:

• Topic 1: Spatial Frictions (Fajgelbaum et al. 2018; Hsieh y Moretti 2019; Moretti 2011)

• Topic 2: Blah (Suárez Serrato y Zidar 2016)

Components

Blocks

Quarto provides dedicated environments for theorems, lemmas, and so forth.

But in presentation format, it’s arguably more effective just to use a Callout Block.

Components

Multicolumn I: Text only

Multicolumn support is very flexible and we can continue with a single full span column in the same slide.

Components

Multicolumn II: Text and figures

Note that sub- and multi-panel figures are also natively supported by Quarto. See here.

Components

Multicolumn III: Code and output

palette("Classic Tableau")

par(
  family = "HersheySans",
  las = 1, pch = 19, cex = 1.5
)

pairs(
  iris[,1:4],
  col=iris$Species
)

Markdown tables

Default table styling

The clean theme rolls its own minimalist aesthetic for tables. This should interface directly with Quarto’s excellent table support.

| fruit  | price  |
|--------|-------:|
| apple  | 2.05   |
| pear   | 1.37   |
| orange | 3.09   |

: Fruit prices {tbl-colwidths="[75,25]"}

Regression tables

Regression example

These aesthetics should carry over to any computation-based tables too.

Let’s take a few slides to illustrate via a simple regression example:

library(fixest)

mods = feols(
  rating ~ complaints + privileges + learning + csw0(raises + critical),
  data = attitude
)

dict = c("rating"     = "Overall Rating",
         "complaints" = "Handling of Complaints",
         "privileges" = "No Special Priviledges",
         "learning"   = "Opportunity to Learn",
         "raises"     = "Performance-Based Raises",
         "critical"   = "Too Critical")

Regression tables

modelsummary

Popular regression table software should play nicely with this theme out of the box. Here’s an example using modelsummary (with the default tinytable backend¹). See the next slide for the resulting table.

library(modelsummary) # Make sure you have >=v2.0.0

modelsummary(
  setNames(mods, c("(1)", "(2)")),
  coef_map = dict, stars = TRUE,
  gof_map = NA
  ) |>
  # some optional stylistic tweaks
  tinytable::group_tt(j = list("Dep. variable: Overall Rating" = 2:3)) |>
  tinytable::style_tt(i = 1:2, j = 2:3, background = "pink")

Regression tables

fixest::etable

Aside: We used the fantastic fixest package to estimate our regression models. fixest bundles its own powerful tabling functions. These were designed for LaTeX output, but can work with this (HTML) theme too.¹

• Set the output: asis R chunk option in your Quarto doc.
• Set the markdown = TRUE fixest::etable option.

```{r}
#| output: asis

setFixest_etable(markdown = TRUE, drop = "Constant")
setFixest_dict(dict)

etable(mods, highlight = .("se" = "complaints"))
```

Regression tables

fixest::etable (cont.)

Figure

Figure

Full-size Figures

You can use the {.background-image} container environment to completely fill the slide background with an image.

Ideally, your figure will be the same aspect ratio as the screen that you’re presenting on.

• This can be a bit tricky because of the dynamic nature of reveal.js / HTML. But it’s probably something close to 16:9.
• Aspect ratio can also matter for a regular full-frame images (previous slide).

Interactive plots

Note: Simple flight data example using threejs. There are many interactive plotting options beyond this. (More details.)

Other

What else can the clean theme do?

We have highlighted some theme-specific components in this demo.

But please note that all of the standard reveal.js functionality and plugins are compatible with the clean theme. This includes:

• chalkboard for annotating slides.
• multiplex for enabling audience navigation of your slides.
• pdf printing in case you don’t have access to a web browser.
• Etc.

Summary

A minimalist and elegant presentation theme

The Quarto reveal.js clean theme aims to be a minimalist and elegant presention theme. Here are some options to get you started.

Add the theme to an existing project.

quarto install extension grantmcdermott/quarto-revealjs-clean

… or, create a new project using our lean template.

quarto use template grantmcdermott/quarto-revealjs-clean

… or, create a new project using these demo slides as a full template.

quarto use template grantmcdermott/quarto-revealjs-clean-demo

Appendix

	Unique	Missing Pct.	Mean	SD	Min	Median	Max	Histogram
rating	22	0	64.6	12.2	40.0	65.5	85.0
complaints	23	0	66.6	13.3	37.0	65.0	90.0
privileges	24	0	53.1	12.2	30.0	51.5	83.0
learning	23	0	56.4	11.7	34.0	56.5	75.0
raises	21	0	64.6	10.4	43.0	63.5	88.0
critical	21	0	74.8	9.9	49.0	77.5	92.0
advance	20	0	42.9	10.3	25.0	41.0	72.0

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